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BIO 2 > AMINO ACIDS AND PROTEINS (LECTURE 1) > Flashcards

AMINO ACIDS AND PROTEINS (LECTURE 1) Flashcards

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1
Q

(protein) monomers are called…

A

amino acids.

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2
Q

(protein) polymers are called… (2)

A

polypeptides or proteins.

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3
Q

amino acids are linked by…

A

peptide bonds.

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4
Q

What is the difference between a protein and a polypeptide? (2)

A

Proteins can be up of 1 or more polypeptides and they serve a function (unlike polypeptides).

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5
Q

List a few protein functions. (5)

A

Enzymes, protein hormones (insulin), transport, cell movement, structural.

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6
Q

Amino acids are made up of 4 components that are all attached to what?

A

A central carbon.

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7
Q

What are the 4 components connected by a central carbon in an amino acid?

A

A hydrogen, a carboxyl group, an amino group and a R group (side chain).

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8
Q

How many different amino acids are there?

A

20

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9
Q

Is the amino group the acidic or basic component of an amino acid?

A

The amino group is the basic component.

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10
Q

Is the carboxyl group the acidic or basic component of an amino acid?

A

The carboxyl group is the acidic component.

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11
Q

What is the significance of the R group (side chain)?

A

The R group is the only varying component for each of the 20 different amino acids and thus determines the characteristics of an amino acid.

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12
Q

What components make up the backbone of an amino acid?

A

The central carbon, the hydrogen, the carboxyl group and the amino group.

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13
Q

How are amino acids classified? (2)

A

As either hydrophobic or hydrophilic.

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14
Q

Hydrophobic amino acids have…

A

non polar side chains.

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15
Q

Hydrophilic amino acids have… (2)

A

polar (but uncharged) side chains or charged side chains.

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16
Q

When is a charged amino acid considered acidic? Is it positively or negatively charged (at pH 7)?

A

When the side chain contains a carboxylic acid (COOH / COO-). It is negatively charged at pH 7 (COO-).

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17
Q

When is a charged amino acid considered basic? Is it positively or negatively charged (at pH 7)?

A

When the side chain contains a amino group (NH2 / NH3+). It is positively charged at pH 7 (NH3+).

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18
Q

The R group of a hydrophobic/non-polar amino acid is usually made up of what? (2)

A

They’re made up of only carbons and hydrogens.

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19
Q

What 2 non-polar amino acids are not made up from only carbon and hydrogen?

A

Methionine (contains S) and tryptophan (contains N).

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20
Q

The R group of a hydrophilic/polar amino usually contains what? What does it certainly lack? (2)

A

They contain oxygen atoms and lack COOH/COO- (carboxylic acids).

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21
Q

Which polar amino acid does not have an oxygen atom? What makes it polar instead?

A

Cysteine is polar because its side chain contains an SH molecule, rather than an oxygen atom.

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22
Q

How can you tell whether the amino acid shown is being shown at pH 7?

A

If the backbone’s amino group is positively charged and the backbone’s carboxyl group is negatively charged, then the amino acid shown is at pH 7.

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23
Q

What chemical formulas can be used to describe an amino acid’s carboxyl and amino groups at pH < 2?

A

NH3+ and COOH

24
Q

What chemical formulas can be used to describe an amino acid’s backbone’s carboxyl and amino groups at pH = 7?

A

NH3+ and COO-

25
Q

What chemical formulas can be used to describe an amino acid’s backbone’s carboxyl and amino groups at pH > 10?

A

NH2 and COO-

26
Q

What characterizes the 3 ionic states in which amino acids can exist?

A

At pH < 2, at pH = 7 and at pH > 10.

27
Q

On what does the overall charge of a protein depend? (2)

A

The sum of the charges of the amino acids is the overall charge of the protein. pH also determines the overall charge.

28
Q

What is the pI of a protein?

A

The isoelectric point (pI) of a protein is the pH at which that protein has a neutral charge.

29
Q

When pH = pI, what is the charge of the protein?

A

neutral

30
Q

When pH > pI, what is the charge of the protein?

A

negative

31
Q

When pH < pI, what is the charge of the protein?

A

positive

32
Q

Amino acids are linked by ____ which are formed by ____ reactions.

A

Amino acids are linked by peptide bonds which are formed by dehydration reactions.

33
Q

Polypeptides have directionality, meaning what?

A

Meaning they have two distinct ends.

34
Q

What names do we give to the ends of a polypeptide?

A

The N-terminus (the amino group) and the C-terminus (the carboxyl group).

35
Q

Why can proteins carry out so many diverse functions in cells?

A

Because there are 20 different amino acids, meaning there are many different possible combinations to make up a protein which means that protein can carry out many different functions.

36
Q

What are the 4 levels of protein structure?

A

Primary structure, secondary structure, tertiary structure and quaternary structure.

37
Q

Describe the primary structure of a protein. (4)

A

It is the linear sequence of amino acids coded for by a gene sequence (and linked by peptide bonds). It is thus determined by the DNA sequence and it has directionality (N terminus to C terminus).

38
Q

Describe the secondary structure of a protein. (3)

A

It is the spatial arrangement of amino acids to form alpha helices or beta sheets. These are formed by the H-bonding between amino (N-H) and carboxyl (C=O) groups of the polypeptide backbone. The R-groups are not involved at this point.

39
Q

Describe the a-helix (alpha helix). (3)

A

There are about 3.6 amino acids per turn. H-bonding occurs between amino acids spaced 4 places apart (aa1-aa5, aa2-aa6, etc.). Side chains are oriented away from the axis (center) of the a-helix.

40
Q

Describe b-sheets (beta sheets). (2)

A

2 regions of the polypeptide chain lie parallel to each other (like a folded sheet). Arrows are used to show a b-sheet’s directionality (n to c terminus).

41
Q

Can the same polypeptide form both a-helices and b-sheets?

A

Yes, it isn’t necessarily one or the other.

42
Q

Do R groups participate in secondary structure bonding? Do they have any impact on the secondary structure at all?

A

No, R groups do not participate in the H-bonding that occurs during the formation of the secondary structure. However, R groups do have an influence on whether a polypeptide will take the shape of an a-helix or/and b-sheets.

43
Q

Describe the tertiary structure of a protein. (3)

A

a-helices and b-sheets interact to form a variety of shapes. These shapes are formed through the interactions between amino acid side chains (R groups). Many tertiary structures are possible.

44
Q

In the formation of a protein’s tertiary structure, what types of interactions occur between the side chains? Which of these is stronger than the other? (2)

A

Side chains interact through covalent (strong) and non-covalent interactions to form the tertiary structure.

45
Q

What are the non-covalent (weak) interactions that can occur during the formation of a protein’s tertiary structure? (4)

A

Hydrogen bonds (between polar amino acids). Hydrophobic interactions (between non-polar amino acids). Van der Waals. Ionic bonds - or - salt bridges (between charged amino acids).

46
Q

What is the covalent (strong) interaction that can occur during the formation of a protein’s tertiary structure? What are some of it’s characteristics? (2 characterisitcs)

A

A disulphide bridge - or - disulphide bond can form, but only between two cysteine amino acids and oxidation is required to make this bond.

47
Q

Describe the quaternary structure of a protein. (2)

A

The quaternary structure of a protein forms when more than one polypeptide chain interact together to form a protein. These polypeptides are held together by the same interactions used to form the tertiary structure.

48
Q

If a protein is composed of 3 subunits, this means that the protein is made up of ____ ____.

A

If a protein is composed of 3 subunits, this means that the protein is made up of 3 polypeptides.

49
Q

Describe the process of denaturation. (2)

A

The denaturation of a protein is the disruption of that proteins structure (unfolding). Only the primary structure is left.

50
Q

Can a denatured protein be renatured? (2)

A

Yes, but it is often difficult to do so.

51
Q

What conditions could denature proteins? (5)

A

Change in temperature, change in pH, presence of salt, presence of a detergent and presence of reducing agents can all denature a protein.

52
Q

In what way does a change in temperature denature proteins?

A

A change in temperature alters the vibrational and rotational energy and disrupts non-covalent interactions such as H-bonds.

53
Q

In what way does a change in pH denature proteins? What does it do to specific side chains?

A

A change in pH changes the ionic state (the charge) of charged side chains.

54
Q

In what way does the presence of salt denature proteins?

A

Salt changes the ionic environment and thus affects ionic bonds within the protein.

55
Q

In what way does the presence of detergents denature proteins? (3)

A

Detergents disrupt hydrophobic interactions. Hydrophobic side chains move from the interior to the exterior of a protein. Hydrophilic side chains move towards the interior of a protein.

56
Q

In what way does the presence of reducing agents denature proteins? Which amino acid does this affect the most?

A

Reducing agents break the covalent disulfide bonds that can form between two cysteine amino acids.

57
Q

Which protein structures are affected by the denaturation of a protein?

A

The secondary, tertiary and quaternary structures are affected by the denaturation of a protein.

BIO 2 (14 decks)

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